61 lines
2.7 KiB
Tcsh
Executable File
61 lines
2.7 KiB
Tcsh
Executable File
#!/bin/tcsh
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source /broad/tools/scripts/useuse
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reuse Python-2.5
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use R-2.11
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setenv DIR /humgen/gsa-hpprojects/GATK/reports
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setenv ARCHIVE_DIR $DIR/archive
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setenv SUMMARY_DIR $DIR/summaries
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setenv DATE `date +"%m_%d_%Y"`
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setenv ARCHIVE $ARCHIVE_DIR/$DATE
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setenv SUMMARY $SUMMARY_DIR/$DATE
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setenv GATK ~/dev/GenomeAnalysisTK/trunk
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setenv GATK_RELEASE_VERSION `ls -l /humgen/gsa-hpprojects/GATK/bin/current | sed 's/.*GenomeAnalysisTK-//'`
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rm -f report.txt
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cd $DIR
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echo "\n####################\nArchiving recently submitted jobs" >> report.txt
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#python $GATK/python/analyzeRunReports.py archive $DIR/submitted -o $ARCHIVE.gz -D >> report.txt
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echo "Released version, all runs" >> report.txt
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#python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --rev $GATK_RELEASE_VERSION >> report.txt
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#python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz -E sting --rev $GATK_RELEASE_VERSION >> report.txt
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python $GATK/python/analyzeRunReports.py summary $ARCHIVE_DIR/*.gz --rev $GATK_RELEASE_VERSION >> report.txt
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python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -E sting --rev $GATK_RELEASE_VERSION >> report.txt
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echo "\n####################\nAll runs" >> report.txt
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python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 >> report.txt
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python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz -E sting --max_days 1 >> report.txt
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echo "\n####################\nLast day, all versions" >> report.txt
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python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 --no-dev >> report.txt
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python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz --max_days 1 -E sting --no-dev >> report.txt
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#echo "Archive directory contents"
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#du -sh $ARCHIVE_DIR
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if (1 == 1) then
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foreach maxDays ( 30 360 )
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echo "Creating table"
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setenv table $ARCHIVE.${maxDays}_days.table
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python $GATK/python/analyzeRunReports.py table $ARCHIVE_DIR/*.gz -o $table --max_days $maxDays
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echo "Creating summary"
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Rscript $GATK/R/GATKRunReport.R $table $SUMMARY.${maxDays}_days.pdf "of previous $maxDays days"
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echo "Creating exception report"
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python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -o $SUMMARY.${maxDays}_days.sting.exceptions.txt --max_days $maxDays -E sting --no-dev
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python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -o $SUMMARY.${maxDays}_days.user.exceptions.txt --max_days $maxDays -E user --no-dev
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rm $table
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end
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endif
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#echo "GATK daily run report" | mutt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK Run report PDFs for $DATE" gsamembers
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cat report.txt | mutt -a report.txt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK run report for $DATE" depristo
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